I recently found a specific explanation for why I keep seeing mysql settings being off in my.cnf and causing load issues.

Recent changes in WHM have added an option to Tweak settings that will allow WHM to determine the “best” settings value. So anytime mysql is restarted from within cpanel, the settings are changed/modified. These settings are on by default.

Allow cPanel & WHM to determine the best value for your MySQL open_files_limit configuration?
This setting’s value defaults to On.

Allow cPanel & WHM to determine the best value for your MySQL max_allowed_packet configuration?
This setting’s value defaults to On.

Allow cPanel & WHM to determine the best value for your MySQL innodb_buffer_pool_size configuration?
This setting’s value defaults to On.

If you are experiencing load issues of unknown origin, this would be something else to check.

Documentation can be found at the below link and is current as of Jun 24, 2016